Buggy code:
public void setLink ( String src ) { } public void setLinkoffline ( String src ) throws TaskException { } public void setLocale ( String src ) { } public void setMaxmemory ( final String max ) { } public void setNodeprecated ( boolean b ) { } public void setNodeprecatedlist ( boolean b ) { } public void setNohelp ( boolean b ) { } public void setNoindex ( boolean b ) { } public void setNonavbar ( boolean b ) { } public void setNotree ( boolean b ) { } public void setOld ( boolean b ) { } public void setOverview ( File f ) { } public void setPackage ( boolean b ) { } public void setPackageList ( String src ) { } public void setPackagenames ( String src ) { } public void setPrivate ( boolean b ) { } public void setProtected ( boolean b ) { } public void setPublic ( boolean b ) { } public void setSerialwarn ( boolean b ) { } public void setSourcefiles ( String src ) throws TaskException { } public void setSourcepath ( Path src ) throws TaskException { } public void setSplitindex ( boolean b ) { } public void setStylesheetfile ( File f ) { } public void setUse ( boolean b ) { } public void setUseExternalFile ( boolean b ) { } public void setVerbose ( boolean b ) { } public void setVersion ( boolean src ) { } public void setWindowtitle ( String src ) { } public void addBottom ( Html text ) { } public void addDoctitle ( Html text ) { } public void addExcludePackage ( PackageName pn ) { } public void addFooter ( Html text ) { } public void addHeader ( Html text ) { } public void addPackage ( PackageName pn ) { } public void addSource ( SourceFile sf ) throws TaskException { } public Path createBootclasspath ( ) throws TaskException { } public Path createClasspath ( ) throws TaskException { } public DocletInfo createDoclet ( ) { } public GroupArgument createGroup ( ) { } public LinkArgument createLink ( ) { } public Path createSourcepath ( ) throws TaskException { } public void execute ( ) throws TaskException { } private String getJavadocExecutableName ( ) { } private void add12ArgIfNotEmpty ( String key , String value ) { } private void addArgIf ( boolean b , String arg ) { } private void evaluatePackages ( Commandline toExecute , Path sourcePath , ArrayList packages , ArrayList excludePackages ) throws TaskException { getLogger ( ) . debug ( ( "Source<seq2seq4repair_space>path<seq2seq4repair_space>=<seq2seq4repair_space>" + ( sourcePath . toString ( ) ) ) ) ; StringBuffer msg = new StringBuffer ( "Packages<seq2seq4repair_space>=<seq2seq4repair_space>" ) ; for ( int i = 0 ; i < ( packages . size ( ) ) ; i ++ ) { if ( i > 0 ) { msg . append ( "," ) ; } msg . append ( packages . get ( i ) ) ; } getLogger ( ) . debug ( msg . toString ( ) ) ; msg . setLength ( 0 ) ; msg . append ( "Exclude<seq2seq4repair_space>Packages<seq2seq4repair_space>=<seq2seq4repair_space>" ) ; for ( int i = 0 ; i < ( excludePackages . size ( ) ) ; i ++ ) { if ( i > 0 ) { msg . append ( "," ) ; } msg . append ( excludePackages . get ( i ) ) ; } getLogger ( ) . debug ( msg . toString ( ) ) ; ArrayList addedPackages = new ArrayList ( ) ; String [ ] list = sourcePath . list ( ) ; if ( list == null ) { list = new String [ 0 ] ; } FileSet fs = new FileSet ( ) ; <START_BUG> fs . setDefaultexcludes ( m_useDefaultExcludes ) ; <END_BUG> Iterator e = packages . iterator ( ) ; while ( e . hasNext ( ) ) { String pkg = ( ( String ) ( e . next ( ) ) ) ; pkg = pkg . replace ( '.' , '//' ) ; if ( pkg . endsWith ( "*" ) ) { pkg += "*" ; } fs . addInclude ( new Pattern ( pkg ) ) ; } e = excludePackages . iterator ( ) ; while ( e . hasNext ( ) ) { String pkg = ( ( String ) ( e . next ( ) ) ) ; pkg = pkg . replace ( '.' , '//' ) ; if ( pkg . endsWith ( "*" ) ) { pkg += "*" ; } final Pattern pattern = new Pattern ( pkg ) ; fs . addExclude ( pattern ) ; } PrintWriter packageListWriter = null ; try { if ( m_useExternalFile ) { m_tmpList = File . createTempFile ( "javadoc" , "" , getBaseDirectory ( ) ) ; toExecute . addArgument ( ( "@" + ( m_tmpList . getAbsolutePath ( ) ) ) ) ; packageListWriter = new PrintWriter ( new FileWriter ( m_tmpList ) ) ; } for ( int j = 0 ; j < ( list . length ) ; j ++ ) { final File source = resolveFile ( list [ j ] ) ; fs . setDir ( source ) ; final DirectoryScanner ds = ScannerUtil . getDirectoryScanner ( fs ) ; final String [ ] packageDirs = ds . getIncludedDirectories ( ) ; for ( int i = 0 ; i < ( packageDirs . length ) ; i ++ ) { File pd = new File ( source , packageDirs [ i ] ) ; String [ ] files = pd . list ( new FilenameFilter ( ) { public boolean accept ( File dir1 , String name ) { if ( name . endsWith ( ".java" ) ) { return true ; } return false ; } }

Fix:
fs . setDefaultExcludes ( m_useDefaultExcludes ) ;